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SIGMA | Strain-level Identification of Genomes from Metagenomic Analysis for Biosurveillance

August 29, 2014. Identification of microbes and accurate estimation of their relative abundance are crucial subjects in metagenomic analysis. Existing taxonomic classification methods are unsuitable for metagenomic biosurveillance due to the following three factors. First, reference genomes including complete genomes of pathogenic bacteria are required. Second, strain-level genome identification from the same species is essential. Third, statistical confidence evaluation of the metagenomi...Nalysis), a n...

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SIGMA | Strain-level Identification of Genomes from Metagenomic Analysis for Biosurveillance | sigma.omicsbio.org Reviews

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August 29, 2014. Identification of microbes and accurate estimation of their relative abundance are crucial subjects in metagenomic analysis. Existing taxonomic classification methods are unsuitable for metagenomic biosurveillance due to the following three factors. First, reference genomes including complete genomes of pathogenic bacteria are required. Second, strain-level genome identification from the same species is essential. Third, statistical confidence evaluation of the metagenomi...Nalysis), a n...

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SIGMA | Strain-level Identification of Genomes from Metagenomic Analysis for Biosurveillance | sigma.omicsbio.org Reviews

https://sigma.omicsbio.org

August 29, 2014. Identification of microbes and accurate estimation of their relative abundance are crucial subjects in metagenomic analysis. Existing taxonomic classification methods are unsuitable for metagenomic biosurveillance due to the following three factors. First, reference genomes including complete genomes of pathogenic bacteria are required. Second, strain-level genome identification from the same species is essential. Third, statistical confidence evaluation of the metagenomi...Nalysis), a n...

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sigma.omicsbio.org

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omicsbio | SIGMA

http://sigma.omicsbio.org/author/omicsbio

All posts by omicsbio. August 29, 2014. Identification of microbes and accurate estimation of their relative abundance are crucial subjects in metagenomic analysis. Existing taxonomic classification methods are unsuitable for metagenomic biosurveillance due to the following three factors. First, reference genomes including complete genomes of pathogenic bacteria are required. Second, strain-level genome identification from the same species is essential. Third, statistical confidence evalu...Nalysis), a n...

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http://sigma.omicsbio.org/73

August 29, 2014. Identification of microbes and accurate estimation of their relative abundance are crucial subjects in metagenomic analysis. Existing taxonomic classification methods are unsuitable for metagenomic biosurveillance due to the following three factors. First, reference genomes including complete genomes of pathogenic bacteria are required. Second, strain-level genome identification from the same species is essential. Third, statistical confidence evaluation of the metagenomi...Nalysis), a n...

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Publications | SIGMA

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Sigma: Strain-level Inference of Genomes from Metagenomic Analysis for Biosurveillance. Strain-level Identification of Genomes from Metagenomic Analysis for Biosurveillance. Proudly powered by WordPress.

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Sigma V1.0.2. GNU GPL 3.0. Strain-level Identification of Genomes from Metagenomic Analysis for Biosurveillance. Proudly powered by WordPress.

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Instructions | SIGMA

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Binaries were built and tested in the Intel architectures (x86 64) running Linux/Unix environment. Sigma package was developed using C . C source codes were compiled and linked by g (gcc version 4.7.2). Please download the last version of Sigma and extract it from the command line. Tar xzvf sigma-version.tar.gz. After you extract the tar ball, please check usage with h option. For example,. Cd Sigma/bin $ ./sigma -h. Please read the user manual to run the Sigma package. Download (PDF, Unknown).

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omicsbio.org

Publications led by collaborators Archives - Omics Bio

http://www.omicsbio.org/category/publications/publications-led-by-collaborators

Publications led by our lab. Publications led by collaborators. Publications on Google Scholar. Category Archives: Publications led by collaborators. Publications in which we are co-authors. Publications led by collaborators. Elevated temperature alters proteomic responses of individual organisms within a biofilm community. July 23, 2014. Mosier, A. C., Zhou Li. Thomas, B. C., Hettich, R. L., Chongle Pan. Banfield, J. F. Doi:10.1038/ismej.2014.113 (2014). [ Link to Article. June 16, 2014. May 22, 2014.

omicsbio.org

metabolomics Archives - Omics Bio

http://www.omicsbio.org/tag/metabolomics

Publications led by our lab. Publications led by collaborators. Publications on Google Scholar. Protocol: how to extract metabolites from fungal and plant samples. October 6, 2014. For the step #6:. Single-use sterile and non-pyrogenic latex-free syringes, 0.01 1 ml Tuberkulin Omnifix-F (B.Braun Melsungen AG, cat. no. 9161406V). 1: Harvest cells and then rapidly freeze the cells in liquid nitrogen. Note: Take care that tissues stay well frozen during homogenization; discard any samples that start to thaw...

omicsbio.org

Sitemap - Omics Bio

http://www.omicsbio.org/sitemap

Publications led by our lab. Publications led by collaborators. Publications on Google Scholar. A list of our publications on scientist journals. More informal and timely communication of our work. Backgrounds and accomplishments of our lab members. Overview of our research projects and facilities. Algorithms and web services developed in our lab. Sigma: http:/ sigma.omicsbio.org. Omega: http:/ omega.omicsbio.org. UniFam: http:/ unifam.omicsbio.org. Sipros: http:/ sipros.omicsbio.org. October 9, 2014.

omicsbio.org

Blog Archives - Omics Bio

http://www.omicsbio.org/category/blog

Publications led by our lab. Publications led by collaborators. Publications on Google Scholar. Protocol: how to extract metabolites from fungal and plant samples. October 6, 2014. For the step #6:. Single-use sterile and non-pyrogenic latex-free syringes, 0.01 1 ml Tuberkulin Omnifix-F (B.Braun Melsungen AG, cat. no. 9161406V). 1: Harvest cells and then rapidly freeze the cells in liquid nitrogen. Note: Take care that tissues stay well frozen during homogenization; discard any samples that start to thaw...

omicsbio.org

Publications led by our lab Archives - Omics Bio

http://www.omicsbio.org/category/publications/publications-led-by-our-lab

Publications led by our lab. Publications led by collaborators. Publications on Google Scholar. Category Archives: Publications led by our lab. Publications in which we are the first author and/or the corresponding author. Publications led by our lab. Functional Phylogenomics Analysis of Bacteria and Archaea using Consistent Genome Annotation with UniFam. October 9, 2014. Kora, G., Tae-Hyuk Ahn. Hyatt, D. and Chongle Pan. 14:207. doi: 10.1186/s12862-014-0207-y (2014). [ Link to Article. September 29, 2014.

omicsbio.org

FAQ Archives - Omics Bio

http://www.omicsbio.org/category/blog/faq

Publications led by our lab. Publications led by collaborators. Publications on Google Scholar. FAQ: is your lab a dry lab or a wet lab? October 2, 2014. FAQ: can we collaborate? October 1, 2014. Omics Technologies for Biological Sciences. Omega for genome assembly. Sigma for biosurveillance and variant calling. UniFam for genome annotation. Omega for transcript assembly. Sigma for transcript quantification. Sipros for protein identification. ProRata for protein quantification. Publications led by our lab.

omicsbio.org

Proteomics Archives - Omics Bio

http://www.omicsbio.org/tag/proteomics

Publications led by our lab. Publications led by collaborators. Publications on Google Scholar. Publications led by our lab. Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community. July 26, 2014. Yao, Q., Justice, N. B., Tae-Hyuk Ahn. Xu, D, Hettich, R. L., Banfield, J. F. and Chongle Pan. 4405, doi:10.1038/ncomms5405 (2014). [ Link to Article. Publications led by collaborators. July 23, 2014. Mosier, A. C., Zhou Li. Banfield, J. F. Publicatio...

omicsbio.org

Lab Members - Omics Bio

http://www.omicsbio.org/people/lab-members

Publications led by our lab. Publications led by collaborators. Publications on Google Scholar. PhD in Computer Science, Virginia Tech, Blacksburg, VA. MS in Electrical and Computer Engineering, Northwestern University, Evanston, IL. BS in Electrical Engineering, Yonsei University, Seoul, Korea. Publications from this lab:. Ahn TH, Chai J, Pan C. Sigma: strain-level inference of genomes from metagenomic analysis for biosurveillance. 4405, doi:10.1038/ncomms5405 (2014). Publications from this lab:. Chai J...

omicsbio.org

Lab Alumni - Omics Bio

http://www.omicsbio.org/people/lab-alumni

Publications led by our lab. Publications led by collaborators. Publications on Google Scholar. PhD in Computer Science, University of Georgia, Athens, GA. MS in Computer Software and Theory, Hohai University, Nanjing, China. BS in Computer Science and Technology, Hohai University, Nanjing, China. Publications from this lab:. Wang, Y., Kora, G., Bowen, B. P. and Pan, C. MIDAS: A Database-Searching Algorithm for Metabolite Identification in Metabolomics. 4405, doi:10.1038/ncomms5405 (2014). Haider, B....

omicsbio.org

Transcriptomics Archives - Omics Bio

http://www.omicsbio.org/tag/transcriptomics

Publications led by our lab. Publications led by collaborators. Publications on Google Scholar. Publications led by collaborators. Elucidation of Zymomonas mobilis physiology and stress responses by quantitative proteomics and transcriptomics. May 22, 2014. Yang, S., Chongle Pan. Hurst, G. B., Dice, L., Davison, B. H. and Brown, S. D. 246, doi:10.3389/fmicb.2014.00246 (2014). [ Link to Article. Publications led by our lab. May 25, 2008. Molecular and cellular proteomics. Omega for genome assembly. Public...

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SIGMA | Strain-level Identification of Genomes from Metagenomic Analysis for Biosurveillance

August 29, 2014. Identification of microbes and accurate estimation of their relative abundance are crucial subjects in metagenomic analysis. Existing taxonomic classification methods are unsuitable for metagenomic biosurveillance due to the following three factors. First, reference genomes including complete genomes of pathogenic bacteria are required. Second, strain-level genome identification from the same species is essential. Third, statistical confidence evaluation of the metagenomi...Nalysis), a n...

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